Thousands of farmers could have GLAS payments delayed again this year because of problems with the Department of Agriculture’s online application system.

Difficulties have been identified with up to 25pc of commonages, planners in the west claim.

Commonage management plans (CMPs) must be drawn up by October 31 if applicants with shareholdings on these lands are to qualify for GLAS payments.

The Irish Natura and Hill Farmers Association (INHFA) has called on the Department to extend the October 31 GLAS applications deadline as a result of the ongoing problems.

A number of planners who contacted the Farming Independent claimed that some commonages were not listed on the online system, others had landowners’ names missing, while some commonages could not be opened.

The Department has admitted in a circular issued to planners recently that commonages were missing from the GLAS system.

“A very small number of commonages remain to be linked to the online system and are not yet available. This work will be completed shortly,” the Department stated.

Despite this admission, the circular insisted that a CMP had to be submitted for each commonage before 2017 payments could be issued to GLAS participants. In response to queries regarding commonages and GLAS applications, the Department confirmed that non-completion of CMPs by October 31 will result in payment delays.

“CMPs not submitted by the deadline of October 31 will result in delayed payment when the 2017 advance payments commence in November,” the Department said.

The Department also insisted that the commonage element of the GLAS application system was working well.

“The commonage system is live and completed CMPs are being submitted on a daily basis,” the Department stated.

But this view has been challenged by planners and by the INHFA. Inishowen-based farm consultant Liam McKinney claimed that he had encountered difficulties with up to 25pc of his commonage applicants.

“We have commonages that are not on the system, we have farmers’ names missing off commonages who were included in interim plans last year, and we have commonages that can’t be opened,” Mr McKinney said.

Similar difficulties have been encountered by Peter Cannon, a planner from Ardara, Co Donegal.

He said the problems have been very frustrating for planners, and were exacerbated by advisors’ inability to make contact with officials in the Department’s GLAS section.

“We can’t make contact with people in the GLAS section, that’s the biggest issue. If they at least told you to go ahead and work on a particular commonage it would be something, but it is very frustrating when you can’t make contact,” Mr Cannon said.

The INHFA has described as “unacceptable” that the Department could penalise farmers for late CMPs.

INHFA president Colm O’Donnell said farmers were being penalised for something that was “outside their control”.

Mr O’Donnell said a payment run which excluded commonage farmers would be “unrealistic” given that the Department’s online system was “not fully functional”, and he called for the October 31 deadline for applications to be extended.

It is understood that plans need to be submitted for around 3,800 commonages nationally, which are farmed by close to 9,000 shareholders.

Over 6,000 farmers will not be paid their GLAS payments as nutrient management plans have not been submitted by advisors, new figures have shown.

Minister of State Andrew Doyle said it was “simply not possible” for the Department to issue the payments.

“6,000 applicants have not met the requirements by not submitting their nutrient management plan. Over 30,000 applicants have submitted the plan and hence have received their balancing payment immediately,” he said.

Over 99pc of 2016 advance payments have issued, with almost €150m paid out under the scheme.